Jon was surprised. But it made some sense. Mikey had made a wish under his breath and disappeared. The wish changed things so he hadn't existed, and Zoe hadn't heard of him--only Jon remembered what had happened before, because of his earlier wish.
"It was the wishing stone," explained Jon.
"What about the wishing stone?" replied Zoe.
"It's lost! You tried to take it..."
"I don't know where it is," said Zoe. "Somewhere near here..." She quickly looked around.
So did Jon, who wanted to get his hands on it first. Maybe it was under that apple tree... Wait a minute, what apple tree?
Guessing what had happened, Jon ran for the apple tree, where in this new reality the stone had, of course, fallen. He found it nestled against the tree trunk, picked it up, and wished "I wish I knew what wish Mikey made and what it did."
Mikey had wished that he and Jon weren't brothers any more. And the wish had turned him into an apple tree.
But of course that wish could be fixed. All Jon had to do was wish that it happened in another way--if Mikey was a girl, they wouldn't be brothers. Maybe he could turn Mikey into a car--Jon had always wanted one. On the other hand, it wasn't urgent. In fact, taking care of Zoe was more urgent. Jon, holding the stone, said "I wish...."